Error in command for generating PCoA plot

[thermokarst]

@Lisa_Crummett

Thank you for your handy detective work Matt. I am sorry that I am keeping you so busy with all of my questions!

No worries - that is what we are here for!

@Lisa_Crummett

The bray_curtis_pcoa_results.qza file was not dependent on any previous metadata files right?

Correct!

@Lisa_Crummett

All values in a custom axis must be numeric, this summary shows the

invalid values and the number of times they were found in column

’Exper.Day’: NaN 17

This is actually an error message coming from Emperor, not from QIIME 2, and what it is saying is that your bray_curtis_pcoa_results.qza file has 17 samples in it that aren't present in your sample metadata file. This make sense, since you mentioned:

this was true several steps back but I deleted those rows so that all of the data was numeric and saved the file as “metadataonlymesocosm2.txt”.

You have a few options:

1. Add the samples back to your metadata file and put some sentinel value in those fields (e.g. -1)
2. Filter the samples that don't have numeric values in their metadata out of your feature table and recompute the core-diversity step using that filtered table.
3. Maybe there is some other option: pinging @yoshiki, for an assist on emperor specifics.

Thanks @Lisa_Crummett!